Project Summary Here, we will test the hypothesis, that myeloid cells have distinct gene expression and epigenetic signatures, which sets the stage to modulate and impair neuronal function in HIV-associated neurocognitive disorders (HAND). Recent studies revealed a possible overlap of HAND with the pathogenesis to Alzheimer?s disease (AD). However, little is known of the molecular mechanisms that lead to the development of HAND. This provides a compelling case to more clearly define the molecular signatures of myeloid cells and neurons in HAND and to elucidate how genetic variation affects gene expression. In recent years, our laboratory has set the stage for a unique and powerful opportunity to gain cell-specific insights into the molecular mechanisms leading to HAND based on archived, human postmortem tissue. We propose the following specific aims: (1) To test whether the gene expression programs of brain myeloid cells and neurons in HAND and AD reflect cellular dysfunction; (2) To identify the epigenetic landscape of myeloid cells and neurons that determine the gene expression profiles in HAND and AD; (3) To determine the causative genetic variants that affect gene expression in individuals with HAND and AD, referred to as quantitative trait loci (QTL). Postmortem brains are the most valuable source for studies of human HAND. We will leverage the resources of the NIH funded National NeuroAIDS tissue consortium and the Shiley-Marcos Alzheimer?s Disease Research Center (ADRC) at UCSD. We will take advantage of our expertise in isolating nuclei from post mortem brain tissue and in sorting for cell type of origin. The transcriptomes of single cell populations will be deciphered by single-nuclei and cell subpopulation specific RNA-seq. To assign regulatory functions to non- coding genomic regions and to identify their interaction networks specifically in neurons or myeloid cells in HAND, we will determine enhancers and open chromatin regions using genome-wide Chromatin- immunoprecipitation followed by sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC)-seq. We will determine the host genetic variants that determine gene expression by performing computational QTL analysis. In concert, the proposed studies are expected to greatly advance our understanding of molecular signatures of myeloid cells and neurons in HAND. In addition, the proposed studies aim to decipher the effects of host natural genetic variation on HAND pathogenesis. Findings based on these studies will define common pathomechanisms in HAND and AD.